Cyb561d2 (cytochrome b561 family, member D2) - Rat Genome Database

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Gene: Cyb561d2 (cytochrome b561 family, member D2) Rattus norvegicus
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Symbol: Cyb561d2
Name: cytochrome b561 family, member D2
RGD ID: 1359644
Description: Predicted to enable heme binding activity; transmembrane ascorbate ferrireductase activity; and transmembrane monodehydroascorbate reductase activity. Predicted to be involved in ascorbate homeostasis. Predicted to be located in vesicle. Predicted to be active in endoplasmic reticulum. Orthologous to human CYB561D2 (cytochrome b561 family member D2); INTERACTS WITH 6-propyl-2-thiouracil; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: cytochrome b-561 domain containing 2; cytochrome b561 domain-containing protein 2; MGC95239; putative tumor suppressor protein 101F6; similar to 101F6 protein; transmembrane ascorbate ferrireductase; transmembrane reductase CYB561D2
RGD Orthologs
Human
Mouse
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88117,091,844 - 117,094,434 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl8117,091,845 - 117,094,366 (-)EnsemblGRCr8
mRatBN7.28108,213,201 - 108,215,778 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8108,213,205 - 108,215,759 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx8113,840,231 - 113,842,758 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08112,039,387 - 112,041,914 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08109,882,168 - 109,884,695 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.08116,295,328 - 116,297,879 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8116,295,329 - 116,297,858 (-)Ensemblrn6Rnor6.0
Rnor_5.08115,651,588 - 115,654,143 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.48112,787,042 - 112,789,564 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera8107,519,621 - 107,522,143 (-)NCBICelera
RGSC_v3.18112,806,497 - 112,809,019 (-)NCBI
Cytogenetic Map8q32NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. The 630-kb lung cancer homozygous deletion region on human chromosome 3p21.3: identification and evaluation of the resident candidate tumor suppressor genes. The International Lung Cancer Chromosome 3p21.3 Tumor Suppressor Gene Consortium. Lerman MI and Minna JD, Cancer Res 2000 Nov 1;60(21):6116-33.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. GOA pipeline RGD automated data pipeline
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:15489334   PMID:17938141   PMID:19734123   PMID:19943161  


Genomics

Comparative Map Data
Cyb561d2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88117,091,844 - 117,094,434 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl8117,091,845 - 117,094,366 (-)EnsemblGRCr8
mRatBN7.28108,213,201 - 108,215,778 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8108,213,205 - 108,215,759 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx8113,840,231 - 113,842,758 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08112,039,387 - 112,041,914 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08109,882,168 - 109,884,695 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.08116,295,328 - 116,297,879 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8116,295,329 - 116,297,858 (-)Ensemblrn6Rnor6.0
Rnor_5.08115,651,588 - 115,654,143 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.48112,787,042 - 112,789,564 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera8107,519,621 - 107,522,143 (-)NCBICelera
RGSC_v3.18112,806,497 - 112,809,019 (-)NCBI
Cytogenetic Map8q32NCBI
CYB561D2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38350,350,862 - 50,354,069 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl350,350,839 - 50,358,460 (+)Ensemblhg38GRCh38
GRCh37350,388,293 - 50,391,500 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map3p21.31NCBI
HuRef350,443,898 - 50,447,100 (+)NCBIHuRef
CHM1_1350,340,572 - 50,343,775 (+)NCBICHM1_1
T2T-CHM13v2.0350,380,585 - 50,383,792 (+)NCBIT2T-CHM13v2.0
Cyb561d2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399107,416,210 - 107,419,392 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9107,416,206 - 107,419,392 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm389107,539,005 - 107,542,193 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9107,539,007 - 107,542,193 (-)Ensemblmm10GRCm38
MGSCv379107,441,342 - 107,444,196 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv369107,397,112 - 107,399,966 (-)NCBIMGSCv36mm8
Celera9107,147,775 - 107,150,630 (-)NCBICelera
Cytogenetic Map9F1NCBI
cM Map958.12NCBI
LOC116907524
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1898,855,719 - 98,858,277 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Cyb561d2
15 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:62
Count of miRNA genes:46
Interacting mature miRNAs:57
Transcripts:ENSRNOT00000031739
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)8105462581132782436Rat
1549909Stresp11Stress response QTL 116.830.0019stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)882352698127352698Rat
631210Bw3Body weight QTL35.9mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight to body weight ratio (CMO:0000654)861019838121662124Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)849849908118871671Rat
9590292Uminl3Urine mineral level QTL 33.620.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)880768445125768445Rat
8694446Bw170Body weight QTL 17012.070.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)880768445125768445Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)870041301121080908Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)868690349119799881Rat
10450865Bw175Body weight QTL 1754.1total fat pad mass (VT:0015008)adipose tissue molecular composition measurement (CMO:0000484)884192326129192326Rat
724539Cm19Cardiac mass QTL 192.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)8103375781129871912Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)8102413464132782436Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)855428333127966348Rat
634332Pia18Pristane induced arthritis QTL 184joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)884192326132782436Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)885348065130348065Rat
631217Activ1Activity QTL 115.9voluntary movement trait (VT:0003491)number of photobeam interruptions in an experimental apparatus (CMO:0001517)8111249511117802327Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)879394435132782436Rat
2313400Anxrr25Anxiety related response QTL 25aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)898145073122898010Rat
8694200Abfw4Abdominal fat weight QTL 49.070.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)880768445125768445Rat
8694392Bw161Body weight QTL 1618.060.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)880768445125768445Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)891340911131690273Rat

Markers in Region
BF396742  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr88117,094,620 - 117,095,173 (+)Marker Load Pipeline
mRatBN7.28108,215,977 - 108,216,530 (+)MAPPERmRatBN7.2
Rnor_6.08116,298,105 - 116,298,657NCBIRnor6.0
Rnor_5.08115,654,365 - 115,654,917UniSTSRnor5.0
RGSC_v3.48112,789,819 - 112,790,371UniSTSRGSC3.4
Celera8107,522,398 - 107,522,950UniSTS
RH 3.4 Map81118.9UniSTS
Cytogenetic Map8q32UniSTS
RH140367  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28108,213,331 - 108,213,507 (+)MAPPERmRatBN7.2
Rnor_6.08116,295,459 - 116,295,634NCBIRnor6.0
Rnor_5.08115,651,719 - 115,651,894UniSTSRnor5.0
RGSC_v3.48112,787,173 - 112,787,348UniSTSRGSC3.4
Celera8107,519,752 - 107,519,927UniSTS
RH 3.4 Map81119.0UniSTS
Cytogenetic Map8q32UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 161 91 90 59 91 59 6 355 191 11 140 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000031739   ⟹   ENSRNOP00000033722
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8108,213,205 - 108,215,716 (-)Ensembl
Rnor_6.0 Ensembl8116,295,329 - 116,297,850 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000082320   ⟹   ENSRNOP00000071082
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl8117,091,845 - 117,094,366 (-)Ensembl
mRatBN7.2 Ensembl8108,213,206 - 108,215,759 (-)Ensembl
Rnor_6.0 Ensembl8116,295,410 - 116,297,858 (-)Ensembl
RefSeq Acc Id: NM_001007753   ⟹   NP_001007754
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88117,091,844 - 117,094,366 (-)NCBI
mRatBN7.28108,213,201 - 108,215,723 (-)NCBI
Rnor_6.08116,295,328 - 116,297,850 (-)NCBI
Rnor_5.08115,651,588 - 115,654,143 (-)NCBI
RGSC_v3.48112,787,042 - 112,789,564 (-)RGD
Celera8107,519,621 - 107,522,143 (-)RGD
Sequence:
RefSeq Acc Id: XM_006243804   ⟹   XP_006243866
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88117,091,844 - 117,094,434 (-)NCBI
mRatBN7.28108,213,201 - 108,215,778 (-)NCBI
Rnor_6.08116,295,328 - 116,297,879 (-)NCBI
Rnor_5.08115,651,588 - 115,654,143 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039081796   ⟹   XP_038937724
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88117,091,844 - 117,094,375 (-)NCBI
mRatBN7.28108,213,201 - 108,215,611 (-)NCBI
RefSeq Acc Id: NP_001007754   ⟸   NM_001007753
- UniProtKB: Q641Y1 (UniProtKB/Swiss-Prot),   A6I2X3 (UniProtKB/TrEMBL),   A0A8L2QHT3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006243866   ⟸   XM_006243804
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000033722   ⟸   ENSRNOT00000031739
Ensembl Acc Id: ENSRNOP00000071082   ⟸   ENSRNOT00000082320
RefSeq Acc Id: XP_038937724   ⟸   XM_039081796
- Peptide Label: isoform X1
Protein Domains
Cytochrome b561

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q641Y1-F1-model_v2 AlphaFold Q641Y1 1-222 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13696267
Promoter ID:EPDNEW_R6791
Type:multiple initiation site
Name:Cyb561d2_1
Description:cytochrome b561 family, member D2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08116,297,837 - 116,297,897EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359644 AgrOrtholog
BioCyc Gene G2FUF-29201 BioCyc
Ensembl Genes ENSRNOG00000021887 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000082320 ENTREZGENE
  ENSRNOT00000082320.2 UniProtKB/Swiss-Prot
Gene3D-CATH 1.20.120.1770 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7133078 IMAGE-MGC_LOAD
InterPro CYB561D1/2 UniProtKB/Swiss-Prot
  Cyt_b561/ferric_Rdtase_TM UniProtKB/Swiss-Prot
KEGG Report rno:363137 UniProtKB/Swiss-Prot
MGC_CLONE MGC:95239 IMAGE-MGC_LOAD
NCBI Gene 363137 ENTREZGENE
PANTHER PTHR15422 UniProtKB/Swiss-Prot
  TRANSMEMBRANE REDUCTASE CYB561D2 UniProtKB/Swiss-Prot
Pfam Cytochrom_B561 UniProtKB/Swiss-Prot
PhenoGen Cyb561d2 PhenoGen
PROSITE CYTOCHROME_B561 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000021887 RatGTEx
SMART B561 UniProtKB/Swiss-Prot
UniProt A0A8L2QHT3 ENTREZGENE
  A6I2X3 ENTREZGENE, UniProtKB/TrEMBL
  C56D2_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-03-20 Cyb561d2  cytochrome b561 family, member D2  Cyb561d2  cytochrome b-561 domain containing 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Cyb561d2  cytochrome b-561 domain containing 2  MGC95239  similar to 101F6 protein  Symbol and Name updated 1299863 APPROVED
2005-07-29 MGC95239  similar to 101F6 protein      Symbol and Name status set to provisional 70820 PROVISIONAL